[REVIEW]: The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images

whedon commented 2 years ago

Submitting author: !--author-handle-->@antoinevacavant@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @lassoan, @deepakri201 Archive: 10.5281/zenodo.6513517

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Status

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Markdown: [![status](https://joss.theoj.org/papers/999c4fe176099cce249b99ddea1b5bc5/status.svg)](https://joss.theoj.org/papers/999c4fe176099cce249b99ddea1b5bc5)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@lassoan & @deepakri201, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @deepakri201

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@antoinevacavant) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot check references

Kevin-Mattheus-Moerman commented 2 years ago

@openjournals/dev Looks like she's dead Jim :point_up:

arfon commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-1-4614-7657-3_19 is OK
- 10.1007/s11517-008-0420-1 is OK
- 10.1109/ipta50016.2020.9286658 is OK
- 10.3390/app11114895 is OK
- 10.1109/icpr48806.2021.9412362 is OK
- 10.1016/j.diii.2019.05.008 is OK
- 10.1038/s41467-021-26216-9 is OK
- 10.1016/j.crad.2013.12.021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant we can now proceed to process this work for acceptance in JOSS. Before we proceed, can you please:

[x] Archive a copy of your repository on ZENODO? You can do so manually but some find these automated steps useful.
[x] Please check that the archive title and author list matches that of the paper. You may need to edit the archive manually for this. At this point you can also add ORCID links and other information if you like.
[x] After you've created and amended the archive, please report back here with the archive DOI.

Thanks.

antoinevacavant commented 2 years ago

Hi @Kevin-Mattheus-Moerman the link with ZENODO is done, the DOI is: 10.5281/zenodo.6513517

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot set 10.5281/zenodo.6513517 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6513517

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant thanks for creating that archived version. Now can you please edit the title and author list so they match the paper?

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot set 1.0.2 as version

editorialbot commented 2 years ago

Done! version is now 1.0.2

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant I've incremented the version tag to match that of the ZENODO archived version. Can you confirm this is correct?

antoinevacavant commented 2 years ago

Yes, this is the correct version (1.0.2)

Kevin-Mattheus-Moerman commented 2 years ago

Great @antoinevacavant, and did you see this question too? :point_down:

@antoinevacavant thanks for creating that archived version. Now can you please edit the title and author list so they match the paper?

antoinevacavant commented 2 years ago

Hi @Kevin-Mattheus-Moerman, well I missed this point, but now the title and authors have been changed according to the paper!

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant it seems that the title for https://zenodo.org/record/6513517 still has not been amended. Can you do this and let me know when it is done? Thanks. FYI if you wanted to add ORCID details for the authors (not a requirement but an option for you) you should be able to do that for the ZENODO archive too.

antoinevacavant commented 2 years ago

@Kevin-Mattheus-Moerman everything's fine now! ;)

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-1-4614-7657-3_19 is OK
- 10.1007/s11517-008-0420-1 is OK
- 10.1109/ipta50016.2020.9286658 is OK
- 10.3390/app11114895 is OK
- 10.1109/icpr48806.2021.9412362 is OK
- 10.1016/j.diii.2019.05.008 is OK
- 10.1038/s41467-021-26216-9 is OK
- 10.1016/j.crad.2013.12.021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3200

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3200, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3201
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03920
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 2 years ago

@antoinevacavant congratulations on getting this work published in JOSS! :tada:

A special thanks to @lassoan and @deepakri201 for their great review efforts! :bow:

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03920/status.svg)](https://doi.org/10.21105/joss.03920)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03920">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03920/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03920/status.svg
   :target: https://doi.org/10.21105/joss.03920

This is how it will look in your documentation:

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